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HYPHY Package >> Feature Additions >> [ADDITION]Model Comparison: MGvsGY http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1107899071 Message started by Sergei on Feb 8th, 2005 at 1:44pm |
Title: [ADDITION]Model Comparison: MGvsGY Post by Sergei on Feb 8th, 2005 at 1:44pm
I have added a standard analysis (builds on Feb 8th or later) which compares the fits of MG94 and GY94 models crossed with an arbitrary nucleotide substituion bias matrix on a codon alignment.
Some of the features: 1). Use exact or approximate branch lengths 2). Tabulate how many sites support MG94 and how many GY94 3). Perform a KH resampling test to assess sampling influence 4). Obtain plots (Mac and Windows versions) of nucleotide and codon frequencies (F1x4, F3x4 and empirical estimators) and site-by-site log likelihoods. 5). Derive profile likelihood confidence intervals on the average dN/dS value. Cheers, Sergei |
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